June 1, 2020

God morgon!

Good morning from Sweden. It’s a new week and a new month! I hope everyone is doing good and staying healthy during these tough times. Like the tradition, today’s digest opens with COVID 19 related articles. There is an interesting Q&A article that provides a lot of important information. There is an article that focused on the disease progression and recovery from COVID in children and found out that Computerized Tomography (CT) may not be the best tool when it comes to analyzing COVID in children. Apart form COVID 19, there is also some new interesting information from the structure of Type-IV pilus. Elsewhere in the digest is an article on an easy to use toolkit for microbiome analysis and development of a new path-breaking point-of-care system for rapid detection of mycobacteria.

Hope you’ll enjoy and learn something new from today’s digest!

COVID 19

Q&A: The novel coronavirus outbreak causing COVID-19 – Dale Fisher and David Heymann – BMC Medicine

Preprint: Structure-based Design of Prefusion-stabilized SARS-CoV-2 Spikes – Ching-Lin Hsieh, et al.

A single-center, retrospective study of COVID-19 features in children: a descriptive investigation – Huijing Ma, et al. – BMC Medicine

Quantifying the impact of physical distance measures on the transmission of COVID-19 in the UK – Christopher I. Jarvis, et al. – BMC Medicine

General Microbiome

Preprint: Microbial strategies for survival in the glass sponge Vazella pourtalesii – Kristina Bayer, et al.

Alterations of gut microbiome accelerate multiple myeloma progression by increasing the relative abundances of nitrogen-recycling bacteria – Xingxing Jian, et al. – Microbiome

Viruses

Preprint: Oropouche virus glycoprotein topology and cellular requirements for virus-like particle assembly – Natalia da silva barbosa, et al.

Bacteria

Preprint: Competition and Caries on Enamel of a Dual-species Biofilm Model of Streptococcus mutans and Streptococcus sanguinis – Natalia Díaz-Garrido, et al.

Preprint: Investigations of dimethylglycine (DMG), glycine betaine and ectoine uptake by a BCCT family transporter with broad substrate specificity in Vibrio species – Gwen Gregory, et al.

Preprint: TsaP binds PilQ and is involved in cyclic di-GMP signaling – Matthew McCallum, et al.

Preprint: SoxS represses flagellar gene expression through RflP in Salmonella enterica Serovar Typhimurium – Srinivas S Thota, et al.

Preprint: Towards Mycobacterium tuberculosis detection at the point-of-care: a brighter solvatochromic probe permits the detection of mycobacteria within minutes – Mireille Kamariza, et al.

Techniques

Preprint: animalcules: Interactive Microbiome Analytics 1 and Visualization in R – W. Evan Johnson, et al.

May 18, 2020

God morgon!

Good morning from Sweden. It’s Monday and the beginning of another week. I am quite excited to write today’s digest because there is a super impressive paper that concerns my area of research. Research efforts in Shigella infections have always suffered from the lack of a mouse model of infection. This notorious bacterium causes enteric infections only in humans and all the infection models, that have been in use so far,  are not physiologically that relevant. It was extremely thrilling to read the development of a mouse model that replicates the typical features of human infections. Talking about infection models, there is another interesting development. A group of researchers has reported an African green monkey model for CoViD-19. This is an important development for clinical assessment of potential vaccine and drug candidates against nCoV-19.

Speaking of vaccines, another group has reported a Neisseria meningitidis outer membrane vesicle (OMV) based vaccine that provides cross-species protection against Neisseria gonorrhoeae. This report assumes great importance when you consider the fact that no Neisseria gonorrhoeae vaccine has entered clinical testing for the past 30 years! In addition to this, there is a structural study of budding in Cryptococcus neoformans that has some really beautiful pictures like this one:

Screenshot 2020-05-18 at 14.57.43

Elsewhere in the digest are some interesting reports on the virulence of a root pathogen, Fusarium; metagenomic identification of diverse viruses; a potent mycobacteriophage; and commentary on Coronaviruses as pathogens responsible for pandemics.

Hope you enjoy today’s selection and have a great week!

COVID-19

Preprint: Establishment of an African green monkey model for COVID-19 – Courtney B. Woolsey, et al.

Preprint: Coronavirus, as a source of pandemic pathogens – Tomokazu Konishi

Bacteria Hysteria

Preprint: NAIP-NLRC4-deficient mice are susceptible to shigellosis – Patrick S Mitchell, et al.

Preprint: The serogroup B meningococcal outer membrane vesicle-based vaccine 4CMenB induces cross-species protection against Neisseria gonorrhoeae – Isabelle Leduc, et al.

Preprint: Antimycobacterial potential of Mycobacteriophage under pathophysiological conditions – Yeswanth C Kalapala, et al.

Preprint: A Division of Labor in the Recruitment and Topological Organization of a Bacterial Morphogenic Complex – Paul D Caccamo, et al.

Preprint: Comparative genomics of ocular Pseudomonas aeruginosa strains from keratitis patients with different clinical outcomes – Kathirvel Kandasamy, et al.

Human gut

Preprint: Higher prevalence of Bacteroides fragilis in Crohn’s disease exacerbations and strain-dependent increase of epithelial resistance – Heike E.F. Becker, et al.

Fungi

Preprint: Let it bud: an ultrastructural study of Cryptococcus neoformans surface during budding events – Glauber R. de S. Araujo, et al.

Methods

Construction of habitat-specific training sets to achieve species-level assignment in 16S rRNA gene datasets – Isabel F. Escapa, et al. – Microbiome

A powerful microbial group association test based on the higher criticism analysis for sparse microbial association signals – Hyunwook Koh and Ni Zhao – Microbiome

Metagenomics

Preprint: Metagenomic identification of diverse animal hepaciviruses and pegiviruses– Ashleigh F. Porter, et al.

Transcriptomics

Preprint: Transcriptome analysis reveals infection strategies employed by Fusarium graminearum as a root pathogen – Yi Ding, et al.

Microbes in the News

Living on The Space Station Leaves a Microbial ‘Fingerprint’ on Astronauts – Science Alert

What are the best foods to increase happiness? – Eastern Daily Press

April 6, 2020

God morgon!

Good morning from Sweden. This is my first post and following the current trend, it starts with some articles on the COVID19 pandemic. Today’s digest is headlined by some interesting preprints reporting inhibitors of SARS-CoV2 virus, followed by another interesting read suggesting the link between the gut microbiome and ADHD, some articles on our struggle against pathogenic bacteria, virus and fungi, and capped off with a small but informative news article on things one should not do during the COVID19 lockdown.

You might notice that today’s post is dominated by preprints. These preprints, while being an excellent way to disperse information as rapidly as it emerges, aren’t peer-reviewed. Hence, always read them with a pinch of salt!

COVID19

Preprint: In vitro screening of a FDA approved chemical library reveals potential inhibitors of SARS-CoV-2 replication – Franck Touret, et al.

Preprint: LY6E Restricts the Entry of Human Coronaviruses, including the currently pandemic SARS-CoV-2 – Xuesen Zhao, et al.

Preprint: Indomethacin has a potent antiviral activity against SARS CoV-2 in vitro and canine coronavirus in vivo – Tianhong Xu, et al.

Preprint: Potent Antiviral Activities of Type I Interferons to SARS-CoV-2 Infection – Emily K. Mantlo, et al.

Microbial interactions

Preprint: Enhanced nutrient uptake is sufficient to drive emergent cross-feeding between bacteria – Ryan K Fritts, et al.

Structure and function of the Arctic and Antarctic marine microbiota as revealed by metagenomics – Weipeng Zhang, et al. – Microbiome

Preprint: Accumulation of dead cells from contact killing facilitates coexistence in bacterial biofilms – Gabi Steinbach, et al.

Human microbiome

Preprint: Gut microbiota from persons with attention-deficit/hyperactivity disorder affects the brain in mice – Anouk C. Tengeler, et al.

Lung function and microbiota diversity in cystic fibrosis – Leah Cuthbertson, et al. – Microbiome

Animal microbiome

Preprint: Functional maturation of the gut microbiota at weaning is influenced by maternal environment in piglets – Martin Beaumont, et al.

Bacteria Hysteria

Preprint: The adaptive transcriptional response of pathogenic Leptospira to peroxide reveals new defenses against infection-related oxidative stress – Crispin Zavala-Alvarado, et al.

Preprint: Cytotoxicity of the effector protein BteA was attenuated in Bordetella pertussis by insertion of an alanine residue – Jan Bayram, et al.

Preprint: Antimicrobial peptide induced-stress renders Staphylococcus aureus susceptible to toxic nucleoside analogues – Alexandro Rodriguez-Rojas, et al.

Preprint: (p)ppGpp and malonyl-CoA set the pace for Staphylococcus aureus adaptation to FASII antibiotics and provide a basis for bi-therapy inhibition – Amit Pathania, et al.

Phages and viruses

Preprint: Viral RNA is a target for Wolbachia-mediated pathogen blocking – Tamanash Bhattacharya, et al.

Preprint: Synchronized infection identifies early rate-limiting steps in the hepatitis B virus life cycle – Anindita Chakraborty, et al.

Techniques

Preprint: Evaluation of DNA extraction protocols from liquid-based cytology specimens for studying cervical microbiota – Takeo Shibata, et al.

Preprint: Biotinylated surfome profiling identifies potential biomarkers for diagnosis and therapy of Aspergillus fumigatus infection – Lei-Jie Jia, et al.

Bioinformatics

Preprint: Interpretable machine learning framework reveals novel gut microbiome features in predicting type 2 diabetes – Wanglong Gou, et al.

Preprint: Comprehensive single cell analysis of pandemic influenza A virus infection in the human airways uncovers cell-type specific host transcriptional signatures relevant for disease progression and pathogenesis – Jenna N Kelly, et al.

MetaEuk—sensitive, high-throughput gene discovery, and annotation for large-scale eukaryotic metagenomics – Eli Levy Karin, et al. – Microbiome

Preprint: Whole genome sequences of multi-drug resistant Escherichia coli isolated in a Pastoralist Community of Western Uganda: Phylogenomic changes, virulence and resistant genes – Jacob Stanley Iramiot, et al.

Microbes in news

News article: Experts study banana disease in Tanzania – The Guardian

News article: What not to do while on COVID-19 lockdown – Jamaica Observer

I know a lot of my fellow researchers are unable to continue their experiments and are yearning to get back to their respective labs. It is a testing time and I believe that patience and perseverance are the biggest strengths of a researcher. So, let’s bank on our strength and hope to see each other on the other side of this global pandemic soon!

With new information emerging every day about COVID19, there is a plethora of misinformation and myths surrounding the virus and the disease. As science enthusiasts, it is pertinent for us to dispel these myths. Here is a small list that I complied a few days back. Check it out!

November 29, 2018

Today’s digest covers updates on human milk oligosaccharides, microbial life in cemetry, intestinal resistome, and benefits of intermittent fasting in human cohort and the gut microbiota in mice.

General microbiome
Next steps in studying the human microbiome and health in prospective studies, Bethesda, MD, May 16–17, 2017 – Rashmi Sinha – Microbiome

Human gut microbiome

Human milk oligosaccharides, milk microbiome and infant gut microbiome modulate neonatal rotavirus infection – Sasirekha Ramani – Nature Communications

Interpersonal Variations in Gut Microbiota Profiles Supersedes the Effects of Differing Fecal Storage Conditions – Caspar Bundgaard-Nielsen – Scientific Reports

In-and-Out Molecular Changes Linked to the Type 2 Diabetes Remission after Bariatric Surgery: An Influence of Gut Microbes on Mitochondria Metabolism – Paulina Samczuk – International Journal of Molecular Sciences

Characterization of fungal dysbiosis in Japanese patients with inflammatory bowel disease – Takayuki Imai – Journal of Gastroenterology

Gut microbiota features of the geographically diverse Indian population – Sudarshan A. Shetty – BioRxiv

Animal experiments

Intermittent administration of a fasting-mimicking diet intervenes in diabetes progression, restores β cells and reconstructs gut microbiota in mice Siying Wei – Nutrition and Metabolism

Skin and gut microbiomes of a wild mammal respond to different environmental cues – Anton Lavrinienko – Microbiome

Mouse intestinal microbiota reduction favors local intestinal immunity triggered by antigens displayed in Bacillus subtilis biofilm – Cédric M. Vogt – Microbial Cell Factories

The murine vaginal microbiota and its perturbation by the human pathogen group B Streptococcus – Alison Vrbanac – BMC Microbiology

Use of next generation sequencing to investigate the microbiota of experimentally induced wounds and the effect of bandaging in horses – Louis J. Kamus – PlosOne

Soil microbiome

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments – Nina Dombrowski – Nature Communications

Built Environment

Microbial life beyond the grave: 16S rRNA gene-based metagenomic analysis of bacteria diversity and their functional profiles in cemetery environments – Akebe Luther King Abia – Science of the Total Environment

Techniques

Prediction of the intestinal resistome by a three-dimensional structure-based method – Etienne Ruppé – Nature Microbiology

Quantitative PCR provides a simple and accessible method for quantitative microbiome profiling – Ching Jian – BioRxiv

Microbes in the news

Poo found on every McDonald’s touchscreen tested – Metro

Non-microbiology picks

Effects of intermittent and continuous calorie restriction on body weight and metabolism over 50 wk: a randomized controlled trial – Ruth Schübel – The American Journal of Clinical Nutrition

 

August 6, 2018

In today’s digest, look for probiotic trials for renal insufficiency and metabolic syndrome, experimental dysbiosis in SIV-infected primates, bacterial and fungal network analyses in soils, and recombination in the human virome. Plus, bacteria in the popular press, hints for scientists using Twitter, the first stem cell therapies for Parkinson’s Disease, and more!

Human gut microbiome
Antigenic mimicry of ubiquitin by the gut bacterium Bacteroides fragilis: a potential link with autoimmune disease – Linda Stewart – Clinical and Experimental Immunology

Animal experiments
Experimental microbial dysbiosis does not promote disease progression in SIV-infected macaques – Alexandra M. Ortiz – Nature Medicine

Addition of dairy lipids and probiotic Lactobacillus fermentum in infant formula programs gut microbiota and entero-insular axis in adult minipigs – Marion Lemaire – Scientific Reports

Animal microbiome
Increased Numbers of Culturable Inhibitory Bacterial Taxa May Mitigate the Effects of Batrachochytrium dendrobatidis in Australian Wet Tropics Frogs – Sara C. Bell – Frontiers in Microbiology

Characterization of the fecal microbiota of healthy horses – Holly L. Stewart – American Journal of Veterinary Research

Plant, root, and soil microbiome
Microbes follow Humboldt: temperature drives plant and soil microbial diversity patterns from the Amazon to the Andes – Andrew T. Nottingham – Ecology

Soil bacterial networks are less stable under drought than fungal networks – Franciska T. de Vries – Nature Communications

Contrasting distribution patterns between aquatic and terrestrial Phytophthora species along a climatic gradient are linked to functional traits – Miguel A. Redondo – The ISME Journal

Variations in microbial community and di-(2-ethylhexyl) phthalate (DEHP) dissipation in different rhizospheric compartments between low- and high-DEHP accumulating cultivars of rice (Oryza sativa L.) – Xue-Xue Chen – Ecotoxicology and Environmental Safety

Water and extremophile microbiome
Evaluation of performance and microbial community successional patterns in an integrated OCO reactor under ZnO nanoparticle stress – Zhenghui Liu – RSC Advances

Screening of quorum quenching activity of the bacteria isolated from dairy industry waste activated sludge – J. Kaur – International Journal of Environmental Science and Technology

Food Microbiology
Identification of Mesophilic Spore-formers in Whey Powder using Shotgun Metagenomic Sequencing – Aoife J. McHugh – Applied and Environmental Microbiology

Probiotics/Prebiotics
An open-label, randomized, placebo-controlled study on the effectiveness of a novel probiotics administration protocol (ProbiotiCKD) in patients with mild renal insufficiency (stage 3a of CKD) – Mariadelina Simeoni – European Journal of Nutrition

Probiotic and synbiotic supplementation could improve metabolic syndrome in prediabetic adults: A randomized controlled trial – Nazila Kassaian – Diabetes & Metabolic Syndrome: Clinical Research & Reviews

Phages and viruses
Investigation of recombination-intense viral groups and their genes in the Earth’s virome – Jan P. Meier-Kolthoff – Scientific Reports

Microbes in the news
Hong Kong Subway Study Shows How Quickly Bacteria Travel Across a City – Gizmodo

Bacteria hysteria
Please Don’t Give Up Your Pet Over The Fear Of Dog-Lick Bacteria – Huffington Post

Science, publishing, and career
Scientists on Twitter: Preaching to the choir or singing from the rooftops? – Isabelle Côté – Facets

Alyson’s non-microbiology picks
‘Reprogrammed’ stem cells to be tested in people with Parkinson’s

These tiny, stretchy speakers and microphones let your skin play music

December 23, 2017

Events and jobs
Assistant Professor of Environmental Microbiology (Tenure-Track) – George Mason University – Fairfax, Virginia, USA
The George Mason University, Department of Environmental Science and Policy (ESP) is seeking an enthusiastic and energetic individual for a Tenure-Track Assistant Professor position in Molecular Environmental Microbiology to supplement existing departmental strengths in applied ecology, aquatic ecology, one health and conservation. This is a full-time, tenure-track position to begin August 2018.

Manager, QC Microbiology – Catalent Pharma Solutions, Inc. – Madison, Wisconsin, USA

Post-Doc – Microbiology & Immunology – Cornell University – Ithaca, NY, USA

Biological Sciences Full-Time Instructor (Microbiology Emphasis) – West Valley-Mission Community College District – Saratoga, CA, USA

General microbiome
Review: Building conventions for unconventional lymphocytes. – Lesley Pasman – Immunological Reviews (from September, but not posted before)

Pregnancy and early life
Gut microbiome in gestational diabetes: a cross-sectional study of mothers and offspring 5 years postpartum – Sayyid Hasan – AOGS

Multi-site human microbiome
Review: The role of microbial amyloid in neurodegeneration. – Robert P Friedland – Plos Pathogens

Human respiratory microbiome
Review: Airway microbiome research: a modern perspective on surveillance cultures? – Damien Roux – Annals Of Translational Medicine

Human skin microbiome
Review: Over a Decade of recA and tly Gene Sequence Typing of the Skin Bacterium Propionibacterium acnes: What Have We Learnt? – Andrew McDowell – Microorganisms

Human oral microbiome
Ecological Balance of Oral Microbiota is Required to Maintain Oral Mesenchymal Stem Cell Homeostasis. – Yingying Su – Stem Cells (Dayton, Ohio)

Shift in the Subgingival Microbiome following Scaling and Root Planing in Generalized Aggressive Periodontitis. – Guojing Liu – Journal Of Clinical Periodontology

Human gut microbiome
Quinones are growth factors for the human gut microbiota. – Kathrin Fenn – Microbiome

Opinion: Microbiome-Germline Interactions and Their Transgenerational Implications. – Michael Elgart – Bioessays : News And Reviews In Molecular, Cellular And Developmental Biology

Review: Modeling metabolism of the human gut microbiome – Stefanía Magnúsdóttir – Current Opinion in Biotechnology

Microbial ecology
Opinion: Engineering microbial communities using thermodynamic principles and electrical interfaces. – Christian Zerfaß – Current Opinion In Biotechnology

Animal experiments
Age-dependent alterations of glucose clearance and homeostasis are temporally separated and modulated by dietary fat. – Mads T F Damgaard – The Journal Of Nutritional Biochemistry

Shift of hindgut microbiota and microbial short chain fatty acids profiles in dairy calves from birth to pre-weaning. – Yang Song – FEMS Microbiology Ecology

Impact of genistein on the gut microbiome of humanized mice and its role in breast tumor inhibition. – Bidisha Paul – Plos One

Tomato Powder Inhibits Hepatic Steatosis and Inflammation Potentially Through Restoring SIRT1 Activity and Adiponectin Function Independent of Carotenoid Cleavage Enzymes in Mice. – Cheng-Chung Li – Molecular Nutrition & Food Research

Faecal microRNAs: indicators of imbalance at the host-microbe interface? – G M Moloney – Beneficial Microbes

Modulation of the fecal microbiota in Sprague-Dawley rats using genetically modified and isogenic corn lines. – Penggao Li – Journal Of Agricultural And Food Chemistry

Sex-dependent impact of Roundup on the rat gut microbiome – Veronica L. Lozano – Toxicology Reports

Effects of garlic-supplemented diet on growth performance and intestinal microbiota of rainbow trout (Oncorhynchus mykiss) – Miray Etyemez Büyükdeveci – Aquaculture

Animal microbiome
Identification and chemical characterization of N acyl-homoserine lactone quorum sensing signals across sponge species and time. – Maya Britstein – FEMS Microbiology Ecology

Reptile-associated Borrelia species in the goanna tick (Bothriocroton undatum) from Sydney, Australia. – Jessica L Panetta – Parasites & Vectors

Multi-Omic Biogeography of the Gastrointestinal Microbiota of a Pre-Weaned Lamb – Antonio Palomba – Proteomes

Identification, comparison and validation of robust rumen microbial biomarkers for methane emissions using diverse Bos Taurus breeds and basal diets – Marc D. Auffret – Frontiers in Microbiology

Plant, root, and soil microbiome
Structure and function of the microbial consortia of activated sludge in typical municipal wastewater treatment plants in winter. – Bo Zhang – Scientific Reports

Key microbial taxa in the rhizosphere of sorghum and sunflower grown in crop rotation. – Tanzelle Oberholster – The Science Of The Total Environment

Metagenomic analysis of soil and freshwater from zoo agricultural area with organic fertilization. – Aylan K Meneghine – Plos One

Field study reveals core plant microbiota and relative importance of their drivers. – Kelly Hamonts – Environmental Microbiology

Enhanced arsenic uptake and polycyclic aromatic hydrocarbon (PAH)-dissipation using Pteris vittata L. and a PAH-degrading bacterium. – Lu Sun – The Science Of The Total Environment

Division of labor during biofilm matrix production – Anna Dragos – bioRxiv

Succession of Fungal and Oomycete Communities in Glyphosate-Killed Wheat Roots – Daniel Schlatter – Phytopathology

Long-term and legacy effects of manure application on soil microbial community composition – Yuting Zhang – Biology and Fertility of Soils

Ammonium nitrogen content is a dominant predictor of bacterial community composition in an acidic forest soil with exogenous nitrogen enrichment – Yanxia Nie – Science of the Total Environment

Water and extremophile microbiome
Consequences of contamination on the interactions between phytoplankton and bacterioplankton. – Goni-Urriza Marisol – Chemosphere

Identification of active denitrifiers by DNA-Stable Isotope Probing and amplicon sequencing reveals Betaproteobacteria as responsible for attenuation of nitrate contamination in a low impacted aquifer. – M Inés Bellini – FEMS Microbiology Ecology

The importance of filamentous cyanobacteria in the development of oxygenic photogranules. – Kim Milferstedt – Scientific Reports

Temperate phages as self-replicating weapons in bacterial competition. – Xiang-Yi Li – Journal Of The Royal Society, Interface (In freshwater metazoan Hydra vulgaris)

The Biogeographical Distribution of Benthic Roseobacter Group Members along a Pacific Transect Is Structured by Nutrient Availability within the Sediments and Primary Production in Different Oceanic Provinces – Marion Pohlner – Frontiers in Microbiology

Organic matter processing by microbial communities throughout the Atlantic water column as revealed by metaproteomics – Kristin Bergauer – PNAS (From November 2017, not posted before)

Homoacetogenesis in Deep-Sea Chloroflexi, as Inferred by Single-Cell Genomics, Provides a Link to Reductive Dehalogenation in Terrestrial Dehalococcoidetes – Holly L. Sewell – mBio

Seasonal and depth-wise variations in bacterial and archaeal groups in the Arabian Sea oxygen minimum zone – Mandar Bandekar – Deep Sea Research Part II: Topical Studies in Oceanography

Review: Microalgae–bacteria biofilms: a sustainable synergistic approach in remediation of acid mine drainage – Sudharsanam Abinandan – Applied Microbiology and Biotechnology

Built environment
Changes in bacterial and archaeal communities during the concentration of brine at the graduation towers in Ciechocinek spa (Poland) – Agnieszka Kalwasińska – Extremophiles

The Coal Seam Microbiome (CSMB) Reference Set, a lingua franca for the microbial coal-to-methane community – Silas H.W. Vick – International Journal of Coal Geology

Food microbiology
Review: Impact of nanosilver on gut microbiota: a vulnerable link. – Dinesh Kumar Dahiya – Future Microbiology

Probiotics / prebiotics
Effects of fermented soymilk with Lactobacillus casei Shirota on skin condition and the gut microbiota: a randomised clinical pilot trial. – T Nagino – Beneficial Microbes

Effect of tablets containing probiotic candidate strains on gingival inflammation and composition of the salivary microbiome: a randomised controlled trial. – M K Keller – Beneficial Microbes

Phages and viruses
Review: Inflammatory Bowel Disease’s Specific Changes of Enteric Mycobiota and Virome. – Yi Chu – Journal Of Digestive Diseases

Review: Phages of life – the path to pharma. – Amanda Forde – British Journal Of Pharmacology

Bioinformatics
Hybrid-denovo: A de novo OTU-picking pipeline integrating single-end and paired-end 16S sequence tags. – Xianfeng Chen – Gigascience

** 3D molecular cartography using LC-MS facilitated by Optimus and ‘ili software. – Ivan Protsyuk – Nature Protocols **

Non-biological synthetic spike-in controls and the AMPtk software pipeline improve fungal high throughput amplicon sequencing data – Jonathan M Palmer – bioRxiv

Multi-omics integration—a comparison of unsupervised clustering methodologies – Giulia Tini – Briefings in Bioinformatics

Review: Genome-scale metabolic networks in time and space – Ove Øyås – Current Opinion in Systems Biology

Techniques
Flow cytometric fingerprinting for microbial strain discrimination and physiological characterization. – Benjamin Buysschaert – Cytometry. Part A : The Journal Of The International Society For Analytical Cytology

Off-axis electron holography of bacterial cells and magnetic nanoparticles in liquid – Tanya Prozorov – Journal of the Royal Society

Microbes in the news
Higher Numbers of 2 Bacteria Species Found in Sarcoidosis Patients, Study Finds – Janet Stewart – Sarcoidosis News

The Surprising Way Your Brain and Gut Are Connected – Julia Malacoff – Shape

Gut Bacteria May Influence Infant Intelligence – Batya Swift Yasgur – MedScape

What Humans Can Learn About Gut Health From Monkey ‘Huddling’ – Francesca Friday – Observer

How to keep your gut healthy over the holidays – Yella Hewings-Martin – Medical News Today

Studies Link Oral Microbiome to Cancers – Pam Harrison – MedPage

Bacteria Found Alive in Earth’s Most Extreme Environments for the First Time Hold Clues to Life on Other Planet – Sydney Pereira – Newsweek

Antibiotic resistance: ‘Sleeping’ bacteria that can survive drug treatment identified – Phys.Org

Bacteria-Basted Supertrees Are Sucking Pollution From Our Waste Sites – James Poulos – Good

Everything you know about toxic shock syndrome is probably wrong – Sara Chodosh – Popular Science

Microbes on the market
Direct-to-consumer DNA and microbiome test launched in Europe – PharmaPhorum

BiomX acquires RondinX to expand microbiome targets for IBD, liver disease – Jonathan Solomon – HealIO

DSM Acquires BioCare Copenhagen to Expand Gut Health Ingredients Portfolio with Probiotics – CISION

Sarcoidosis Industry Overview with Total Market Share and Distribution of Sarcoidosis for 7 MM for 2025 – Miltech

Global Human Microbiome Market Analysis, Share, Production, Growth, Trends and Forecast 2017 to 2022 – Arun P. – GeoPolMonitor

Global Microbiome Therapeutic Market Outlook – Johnson and Johnson, AB-Biotics, Vedanta Biosciences, AbbVie Inc – Kevin Harper – The News Columnist

Bacteria Hysteria
‘This is how the X-Men started’: Internet shocked by astronaut discovery of ‘alien bacteria’ on International Space Station – Sarah K. Burris – RawStory

Science, publishing, and career
Graduate Biomedical Science Education Needs a New Philosophy – Gundula Bosch – mBio

November 28, 2017

Identification of nitrite-oxidizing bacteria important for dark ocean carbon fixation, effects of antibiotic exposure to the maternal gut microbiota extend to offspring in mice and enhance colitis, a review on genome mining for natural products discovery.

Events and jobs

Postdoc position on biofilm-mediated co-evolution of industrial strains – Biologisk Institut, University of Copenhagen, Denmark

Human skin microbiome

Measuring the microbiome of chronic wounds with use of a topical antimicrobial dressing – A feasibility study – Lindsay Kalan – PLOS ONE

Human gut microbiome

Pre-print: Endospores and other lysis-resistant bacteria comprise a widely shared core community within the human microbiota – Sean M Kearney – bioRxiv

Opinion: Human Gut Microbiome: Function Matters – Anna Heintz-Buschart – Trends in Microbiology

Review: The gut microbiome, symptoms, and targeted interventions in children with cancer: a systematic review – Jinbing Bai – Supportive Care in Cancer

Animal experiments

Intergenerational transfer of antibiotic-perturbed microbiota enhances colitis in susceptible mice – Anjelique F Schulfer – Nature Microbiology

Canagliflozin reduces plasma uremic toxins and alters the intestinal microbiota composition in a chronic kidney disease mouse model – Eikan Mishima – American Journal of Physiology, Renal Physiology

Insect-based diet, a promising nutritional source, modulates gut microbiota composition and SCFAs production in laying hens – Luca Borrelli – Scientific Reports

Animal microbiome

Comparison of the gut microbiota composition between wild and captive sika deer (Cervus nippon hortulorum) from feces by high-throughput sequencing – Yu Guan – AMB Express

Plant, root, and soil microbiome

Pre-print: The effects of host species and sexual dimorphism differ among root, leaf and flower microbiomes of wild strawberries in situ – Na Wei – bioRxiv

Water and extremophile microbiome

Major role of nitrite-oxidizing bacteria in dark ocean carbon fixation – Maria G Pachiadaki – Science

Investigating the bacterial community and amoebae population in rural domestic wastewater reclamation for irrigation – Bingjian Cui – Journal of Environmental Sciences

Phages and viruses

Review: Viruses of archaea: Structural, functional, environmental and evolutionary genomics – Mart Krupovic – Virus Research

Bioinformatics

Review: Omics-based natural product discovery and the lexicon of genome mining – Henrique Machado – Current Opinion in Microbiology

More microbes

Chromosome level assembly and secondary metabolite potential of the parasitic fungus Cordyceps militaris – Glenna J Kramer – BMC Genomics

Genomic assessment in Lactobacillus plantarum links the butyrogenic pathway with glutamine metabolism – Cristian Botta – Scientific Reports

Microbes in the news

Researchers conduct novel wheat microbiome analysis under four management strategies – Phys.Org

Fertility clinics treat abnormal vaginal bacteria aiming to improve reproductive outcome – Medical Xpress

Microbe threat to Mars – Andrew Masterson – Cosmos

Flies’ Feet Can Spread Bacteria – Kerry Grens – The Scientist

Despite Their Tiny Genome, A Beetle’s Bacteria Pack A Big Punch – Julianna LeMieux – American Council on Science and Health

CRISPR Harnessed to Turn Bacteria into Microscopic Tape Recorders – Genetic Engineering & Biotechnology News

Bacteria hysteria

Warning: Those lipstick samples could be loaded with poop, investigation finds – Mandy Matney – Sacramento Bee

Science, career, and publishing

Pre-print: A design framework and exemplar metrics for FAIRness – Mark D Wilkinson – bioRxiv